HPTN 069/ACTG A5305 was a study of 48-week oral PrEP regimens in MSM and transgender women A rectal substudy was included to evaluate drug concentrations in rectal compartment vs. blood, gut-associated lymphoid tissue (GALT) responses to four antiretroviral (ARV) PrEP regimens (maraviroc (MVC), MVC + emtricitabine (FTC), MVC + tenofovir disoproxil fumarate (TDF), and TDF + FTC), and to determine whether ARV exposure was associated with ex vivo suppression of HIV infection in colorectal explants. Methods: CCR5 genotype was characterized using PCR. At baseline and at weeks 24, 48, and 49, GALT phenotype was characterized by flow cytometry, rectal biopsies were challenged with HIV-1 BaL , and tissue and plasma pharmacokinetics were measured via mass spectrometry. Results: Exposure to MVC was not associated with increased expression of CD4+/CCR5+ HIV target T-cells. Significant ex vivo viral suppression compared to baseline was seen at Weeks 24 and 48, ranging from 1.4 to 1.8 log 10 for all study regimens except the MVC-alone arm which did not show statistically significant viral suppression at Week 48. Tissue concentrations of tenofovir (TFV), TFV-diphosphate (DP), and FTC were correlated with viral suppression. Conclusions: MVC-containing HIV PrEP regimens did not increase GALT CD4+ T-cell activation or the CD4+/CCR5+ phenotype. No virologic suppression was seen with MVC-alone at Week 48 compared to combination regimens, suggesting MVC monotherapy might be less effective than combination ARV PrEP regimens.